Genomic and Transcriptomic Analysis Identified Novel Putative Cassava lncRNAs Involved in Cold and Drought Stress

Suksamran, Rungaroon; Saithong, Treenut; Thammarongtham, Chinae; Kalapanulak, Saowalak

doi:10.3390/genes11040366

Cited by 25 publications

(7 citation statements)

References 79 publications

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“…LncRNAs work as cis -acting elements near the RNA synthesis sites ( Zhao et al, 2020b ). Further, trans -acting factors, they can also work away from synthesis sites ( Suksamran et al, 2020 ). LncRNAs transcribed by polymerase II, III, IV, and V. They are further divided into five categories depending on their positions in genome near or away from protein-coding genes.…”

Section: Mechanismmentioning

confidence: 99%

Moving Beyond DNA Sequence to Improve Plant Stress Responses

Saeed

Chaudhry²,

Bakhsh³

et al. 2022

Front. Genet.

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Plants offer a habitat for a range of interactions to occur among different stress factors. Epigenetics has become the most promising functional genomics tool, with huge potential for improving plant adaptation to biotic and abiotic stresses. Advances in plant molecular biology have dramatically changed our understanding of the molecular mechanisms that control these interactions, and plant epigenetics has attracted great interest in this context. Accumulating literature substantiates the crucial role of epigenetics in the diversity of plant responses that can be harnessed to accelerate the progress of crop improvement. However, harnessing epigenetics to its full potential will require a thorough understanding of the epigenetic modifications and assessing the functional relevance of these variants. The modern technologies of profiling and engineering plants at genome-wide scale provide new horizons to elucidate how epigenetic modifications occur in plants in response to stress conditions. This review summarizes recent progress on understanding the epigenetic regulation of plant stress responses, methods to detect genome-wide epigenetic modifications, and disentangling their contributions to plant phenotypes from other sources of variations. Key epigenetic mechanisms underlying stress memory are highlighted. Linking plant response with the patterns of epigenetic variations would help devise breeding strategies for improving crop performance under stressed scenarios.

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Section: Mechanismmentioning

confidence: 99%

Moving Beyond DNA Sequence to Improve Plant Stress Responses

Saeed

Chaudhry²,

Bakhsh³

et al. 2022

Front. Genet.

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“…LncRNAs can act as key genetic and epigenetic regulators of gene expression (Karlik et al, 2019). They may function as cisacting elements by working near the site of RNA synthesis, acting directly on consecutive genes on the same strand (Zhao et al, 2020; Figure 1A); or as trans-acting factors by operating far from the site of synthesis (Suksamran et al, 2020; Figure 1B). LncRNAs may interfere with the binding of transcription factors to promoter regions (Csorba et al, 2014).…”

Section: Lncrnas As Precursors In Rddm Silencing Pathwaymentioning

confidence: 99%

“…The lncRNA TahlnRNA27 was induced under heat treatment and characterized as putative miRNA precursor by presenting Ta-miR2010 family sequences (Xin et al, 2011). Similarly, 182 novel cold-responsive lncRNAs are known to be differentially expressed in cassava (Suksamran et al, 2020); whereas 2,271 lncRNAs were cold-responsive in alfalfa (Zhao et al, 2020).…”

Section: Lncrna In Crop Plantsmentioning

confidence: 99%

“…To improve crop performance in regions limited by water deficit, studies have been conducted to investigate the droughtresponsive lncRNAs in crop species including foxtail millet (Qi et al, 2013); maize (Zhang et al, 2014); rice (Chung et al, 2016); wheat (Cagirici et al, 2017); tomato (Eom et al, 2019); and cassava (Suksamran et al, 2020). A recent work carried out with maize identified 124 drought-responsive lncRNAs characterized as cis-acting factors (Pang et al, 2019).…”

Section: Lncrna In Crop Plantsmentioning

confidence: 99%

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From Trash to Luxury: The Potential Role of Plant LncRNA in DNA Methylation During Abiotic Stress

2021

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Remarkable progress has been made in elucidating important roles of plant non-coding RNAs. Among these RNAs, long noncoding RNAs (lncRNAs) have gained widespread attention, especially their role in plant environmental stress responses. LncRNAs act at different levels of gene expression regulation, and one of these mechanisms is by recruitment of DNA methyltransferases or demethylases to regulate the target gene transcription. In this mini-review, we highlight the function of lncRNAs, including their potential role in RNA-directed DNA Methylation (RdDM) silencing pathway and their potential function under abiotic stresses conditions. Moreover, we also present and discuss studies of lncRNAs in crops. Finally, we propose a path outlook for future research that may be important for plant breeding.

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“…They observed that csd1, csd2 and ccsmutanten showed a higher heat stress tolerance than wild-type plants, combined with an increased accumulation of heat stress transcription factors and heat shock proteins as well as much less damage to plants (Guan et al, 2013). Corn (Yu et al, 2018) and cassava (Suksamran et al, 2020) responds to abiotic stress such as heat, cold, salt, and drought.…”

Section: Cold and Heat Stress Tolerancementioning

confidence: 99%

Advances on the application of non-coding RNA in crop improvement

Dekeba¹

2021

Afr. J. Biotechnol.

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Thanks to committed plant breeding researchers over the few decades, many problems associated with food supply and qualities have been improved. Food security is an exceptionally serious worldwide issue via world climate change, the increase in human population, and the use of plants for bioethanol production in current years. Improved tolerance to abiotic and biotic stress, resistance to herbicides, improved yield, and plants with wonderful nutritional value are essential goals of crop improvement. RNAi applications are the modern innovation that can assist in the solution for these issues. A natural protection mechanism against invading viruses, nucleic acids, and transposons non-coding RNAs (ncRNAs), are identified as effector molecules in RNA-mediated gene silencing and used in the genetic modification of crops. These ncRNAs are concerned with the regulation of growth, development, and response to stress at the transcriptional and translational levels. Improving crop yields is the final purpose of molecular plant breeding. ncRNAs, along with transfer RNAs (tRNAs) and ribosomal RNAs (rRNAs), as well as small non-coding RNAs (sncRNAs) and the long non-coding RNAs (lncRNAs), have been recognized as essential regulators of gene expression in plants in plant immunity and adaptation to abiotic and abiotic stages biotic stress.

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Genomic and Transcriptomic Analysis Identified Novel Putative Cassava lncRNAs Involved in Cold and Drought Stress

Cited by 25 publications

References 79 publications

Moving Beyond DNA Sequence to Improve Plant Stress Responses

Moving Beyond DNA Sequence to Improve Plant Stress Responses

From Trash to Luxury: The Potential Role of Plant LncRNA in DNA Methylation During Abiotic Stress

Advances on the application of non-coding RNA in crop improvement

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